You're welcome.
Not sure why is this, since one would think we can always download the application but customization and data are the only important info, which is not backed up. If it was backed up, then it will collide with each user's info.
The backup iTunes creates and maintains for the iPhone includes data such as most iPhone settings, email account settings, contact info, SMS messages, notes, recent calls, call favorites, photos in the iPhone's camera roll, and 3rd party app settings and data created and stored by a 3rd party app.
The backup is updated if needed as the first step during the sync process - if any of data on the iPhone that is included with the backup has changed since the last sync, which is usually 100% of the time.
This is for each iPhone based on the name of the iPhone - more than likely your iPhone and your wife's iPhone will not have the same name. When syncing more than one iPhone with iTunes on the same computer, the backup for each iPhone is kept separate and does not collide with another iPhone.
You and your wife can install the same app. You and your wife can have different settings for the app on each other's iPhone. If the app creates and stores data, you and your wife can have different data for the app on each other's iPhone. When you sync your iPhone, your iPhone's backup will include the settings for the app, and data created and stored by the app on your iPhone. When your wife syncs her iPhone, her iPhone's backup will include the settings for the app, and data created and stored by the app on her iPhone.
This will not collide with the same app installed on each iPhone. App settings, and data created and stored by an app is not stored with the app in iTunes.